Who’s related to fruit flies?

I’ve spent my entire life as an academic working with “fruit flies” in the genus Drosophila. (Note that the true fruit flies are not Drosophila, but rather members of family Tephritidae, which includes the much-feared Mediterranean fruit fly. Drosophila are more accurately called “vinegar flies”.) Drosophila is surely the best-studied genus of insects, at least from an evolutionary and genetic point of view. Most people don’t realize, when I tell them or show them what I work on, that many of the principles of modern genetics, including sex linkage and the physical linkage of genes on chromosomes, came from research on Drosophila.

Flies (insects of the order Diptera) are important numerically and in relation to humans. One in ten of all named multicellular species, and that includes plants, are flies: Diptera contains 152,000 named species and many more that are undescribed. And they are of medical and agricultural importance, for Diptera includes mosquitoes, tsetse flies, Medflies, horseflies, botflies and, of course, houseflies. But up to now, the family tree of flies—and of my beloved Drosophila—has been contentious. Drawing family trees using morphological traits—body parts and the like—has been helpful, but the higher-order relationships remained mysterious.

Diptera is indeed “monophyletic”; that is, the group contains all living descendants of a single common ancestor.

A new and unexpected finding: the oldest groups (or, as the authors call them, “the earliest extant fly lineages”) are semi-aquatic: they are two families (Deuterophlebiidae and Nymphomyiidae) in which both larvae and adults are associated with water. These habits, and similar aquatic tendencies in nearby dipteran groups, suggest that the ancestors of all modern flies were also semi-aquatic. The authors call the Deuterophlebiidae and Nymphomyiidae “rare and anatomically bizarre.” Here’s a Nymphomyia alba adult and larva:

There were three large radiations of flies, characterized not such much by higher rates of species formation, but lower rates of extinction.

And, of greatest interest to me, they found two groups that appear to be the closest relatives of Drosophilidae (the family that contains Drosophila and allied genera). First, here’s a fly that I’ve worked on for years: the undergraduate genetics star Drosophila melanogaster:

Molecular data showed, surprisingly, that the closest relatives of Drosophila (by this I mean the sister groups of the family Drosophilidae) are two strange groups, the Braulidae (bee lice) and the Cryptochetidae. Here’s the authors’ phylogeny:

Bee lice are bizarre wingless flies that are parasites; they cling to bees (one per bee, except for the queen, who can have many), and their larvae live on honey from the hive. They’re not regarded as major bee pests unless there’s a serious infestation of a hive. Here’s the bee louse fly Braula coeca; you can see that it doesn’t look at all like a fly, for its wings are gone and it looks for all the world like a louse (lice are in a completely different order of insects, the Phthiraptera).

This is a FLY!

Here’s a true louse, one that some of us may have had—the pubic louse Phtirus pubus. The resemblance between this and the fly above is a great example of convergent evolution. Parasitic clinging insects don’t need wings, and develop bodies and legs good for holding onto insect setae (bristles) and hairs:

Here’s some bee louse flies on a queen. The flies are about the size of a small pinhead:

The other group of Drosophila relatives, the Cryptochetidae, look more conventional as adults, but their larvae are also parasites—in this case endoparasites of scale insects. The larvae have been used as biocontrol agents.

The rest of the paper’s results will excite systematists and entomologists, but won’t thrill the rest of us. But they’re solid results, since they’re based on lots of molecular data and the branch positions are well supported. In the next post we’ll see how creationists have taken this paper and, in trying to show their fellow Jebus-lovers that its results—and evolution itself—are wrong, have wilfully misunderstood and distorted what the paper showed.

Molecular data showed, surprisingly, that the closest relatives of Drosophila are two strange groups, the Braulidae (bee lice) and the Cryptochetidae.

I have always found the term ‘closest relative’ in cladograms potentially misleading. In theory the branch leading to the Braulidae + Cryptochetidae (BC) clade could be so long that the distance from the Drosophilidae to the Camillidae (for example) could be shorter than the distance from the Drosophilidae to the BC clade. Would in that case the Camillidae not be the closest relatives of the Drosophilidae? To avoid this ambiguity I think the term ‘sister group’ is preferable to ‘closest relative’.

In theory the branch leading to the Braulidae + Cryptochetidae (BC) clade could be so long that the distance from the Drosophilidae to the Camillidae (for example) could be shorter than the distance from the Drosophilidae to the BC clade. Would in that case the Camillidae not be the closest relatives of the Drosophilidae?

No. Not sure what units your branch-lengths are in, but that doesn’t matter anyway. The closeness of relation of two taxa is a function solely of the recency of their common ancestor. Even if braulids and/or cryto…ids were the product of some crazy burst of rapid evolution, the common ancestor of drosophids and B+C was still more recent than than the common ancestor of Drosophila and anything else (on the phylogeny shown).

Phylogenies are no longer about all similarities, just the shared-derived ones.

Even when you only look at shared-derived characters, A and C can be more similar than A and B, while A and B are nevertheless sister groups. Sharing a more recent common ancestor is of course the fundamental criterion used to group A and B together. I don’t dispute that at all. It is just that I don’t like to express this by saying that A and B are each others closest relatives, because ‘closest’ can easily be misread as ‘most similar’ (nearest in terms of genetic distance, measured using some aligned sequence).

Well, except for some specimens in Dr. Venter’s labs, as best we know, every living organism on the planet now and for the past few billion years.

That writ, Rutherford’s quote about physics v stamp collecting comes to mind. This is some heavy-duty stamp collecting. It makes me think that we’re at the dawn of a new age in biology, one that’s poised to change in radical and exciting new ways. This much of a quantitative leap in our ability to categorize things, combined with our new tools for information analysis, seems poised to lead us to new insights not even imaginable to earlier generations.

When physicists go stamp collecting, they sort through vast piles of stamps just to find one or two special ones, like the Higgs. They’ve made that kind of large-scale automated stamp collecting their specialty. Before the modern age of DNA sequencing, that sort of technique has been unavailable to biologists…but not any longer.

We are undoubtedly living through a biological revolution. Sequence data are available from hundreds of thousands of organisms (not whole genomes, but still!), and what’s more, you can SEARCH them. So you can study, say, the history of genes associated with the sense of smell. It’s quite amazing. Any budding evolutionary biologists out there – get into bioinformatics. However, for resolving the questions to do with deep evolutionary time, we’ll need more than just more sequences, as this recent free perspective piece by Hervé Philippe makes clear:

(Note that the true fruit flies are not Drosophila, but rather members of family Tephritidae, which includes the much-feared Mediterranean fruit fly. Drosophila are more accurately called “vinegar flies”.)

So, on what grounds exactly does one argue that a common name–governed by use rather than by a formalized code–is usually used incorrectly? I’d thought prescriptive definitions were basically dead in the context of natural language.

[…] phylogeny is the definitive answer because the researchers used an ever increasing number of genes. One influential blogger, who’s also an evolutionary entomologist, summarized the results of the Diptera tree of life as such: But they’re solid results, since […]

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